The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]>; Discussion list for GROMACS users <[email protected]> Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: > Hi, > I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. > > For the step of solvation I ran this command: > # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top > > The output of this step is as here: > Reading solute configuration > frame t= 1.000 > Containing 17503 atoms in 3800 residues > Initialising van der waals distances... > > WARNING: masses and atomic (Van der Waals) radii will be determined > based on residue and atom names. These numbers can deviate > from the correct mass and radius of the atom type. > > Reading solvent configuration > "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" > solvent configuration contains 648 atoms in 216 residues > > Initialising van der waals distances... > Will generate new solvent configuration of 4x4x4 boxes > Generating configuration > Sorting configuration > Found 1 molecule type: > SOL ( 3 atoms): 13824 residues > Calculating Overlap... > box_margin = 0.315 > Removed 10608 atoms that were outside the box > Neighborsearching with a cut-off of 1.125 > Table routines are used for coulomb: FALSE > Table routines are used for vdw: FALSE > Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 > System total charge: 0.000 > Grid: 18 x 18 x 18 cells > Successfully made neighbourlist > nri = 152829, nrj = 41861902 > Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. > Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. > Added 252 molecules > Generated solvent containing 756 atoms in 252 residues > Writing generated configuration to system_solv.gro > > Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# > frame t= 1.000 > > Output configuration contains 18259 atoms in 4052 residues > Volume : 272.811 (nm^3) > Density : 947.87 (g/l) > Number of SOL molecules: 3907 > > Processing topology > Removing line #929 'SOL 533' from topology file (topol.top) > > > > Then running grompp for the next step ( neutralization ) > > grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr > > But the error is: > > Fatal error: > number of coordinates in coordinate file (system_solv.gro, 18259) > does not match topology (topol.top, 18159) > For more information and tips for troubleshooting, please check the GROMACS > > > Would you pleas help me? Do I need to modify the .top file before running > grompp? > Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
